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kopardev/README.md

Profile views in 2022

Life is so short, but DNA is so long ...

Welcome! My name is Vishal Koparde ( pronouced as We-shall Co-Par-Day ).

I actively contribute code to numerous repos:

Vishal's GitHub stats

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PubMed Summary

List of recent scientific contributions:

Title Publication Year DOI
Loss of tumor suppressors promotes a non-cell-autonomous inflammatory response and enhances LAG3+T cell mediated immune suppression Accepted at Nat. Comms. 2024 TBD
DNAJC9 prevents CENP-A mislocalization and chromosomal instability by maintaining the fidelity of histone supply chains EMBOJ 2024 https://doi.org/10.1038/s44318-024-00093-6
Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection EMBO Rep. 2024 https://doi.org/10.1038/s44319-023-00051-z
Chromatin accessibility landscape of human triple-negative breast cancer cell lines reveals variation by patient donor ancestry Cancer Research Communications 2023 https://doi.org/10.1158/2767-9764.CRC-23-0236
SMYD3 represses tumor-intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck Cell Reports 2023 https://doi.org/10.1016/j.celrep.2023.112823
The transcription factor EGR2 controls homing and pathogenicity of TH17 cells in the central nervous system Nature Immunology 2023 https://doi.org/10.1038/s41590-023-01553-7
Transcriptional landscape of Kaposi sarcoma tumors identifies unique immunologic signatures and key determinants of angiogenesis Journal of Translational Medicine 2023 https://doi.org/10.1186/s12967-023-04517-5
A virus-induced circular RNA maintains latent infection of Kaposi’s sarcoma herpesvirus PNAS 2023 https://doi.org/10.1073/pnas.2212864120
Alternative splicing and circRNA biogenesis driven by alpha and gamma herpesviruses Submitted to Nature Communications 2022 bioRxiv
Antisense transcription from lentiviral gene targeting linked to an integrated stress response in colorectal cancer cells Molecular Therapy 2022 https://doi.org/10.1016/j.omtn.2022.05.029
Unique roles of vaginal Megasphaera phylotypes in reproductive health Microbial Genomics 2021 https://doi.org/10.1099/mgen.0.000526
PERK signaling through C/EBPδ contributes to ER stress-induced expression of immunomodulatory and tumor promoting chemokines by cancer cells Cell Death & Disease 2021 https://doi.org/10.1038/s41419-021-04318-y
Ubiquitination of MHC Class II by March-I Regulates Dendritic Cell Fitness The Journal of Immunology 2021 https://doi.org/10.4049/jimmunol.2000975
Characterizing expression and regulation of gamma-herpesviral circular RNAs Frontiers in microbiology 2021 https://doi.org/10.3389/fmicb.2021.670542
Identifying and characterizing virus-encoded circular RNAs Methods 2021 https://doi.org/10.1016/j.ymeth.2021.03.004
Loss of myeloid-specific lamin A/C drives lung metastasis through Gfi-1 and C/EBPε-mediated granulocytic differentiation Molecular carcinogenesis 2020 https://doi.org/10.1002/mc.23147
Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy Nature medicine 2019 https://doi.org/10.1038/s41591-019-0465-8
The vaginal microbiome and preterm birth Nature medicine 2019 https://doi.org/10.1038/s41591-019-0450-2
Multi-omic Microbiome Profiles in the Female Reproductive Tract in Early Pregnancy Infectious Microbes & Diseases 2019 https://doi.org/10.1097/IM9.0000000000000007
Head and neck squamous cancer progression is marked by CLIC4 attenuation in tumor epithelium and reciprocal stromal upregulation of miR-142-3p, a novel post-transcriptional regulator of CLIC4 Oncotarget 2019 https://doi.org/10.18632/oncotarget.27387
Rbfox1 up-regulation impairs BDNF-dependent hippocampal LTP by dysregulating TrkB isoform expression levels Elife 2019 https://doi.org/10.7554/eLife.49673.001
Single chromosome aneuploidy induces genome-wide perturbation of nuclear organization and gene expression Neoplasia 2019 https://doi.org/10.1016/j.neo.2019.02.003
Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence BMC genomics 2018 https://doi.org/10.1186/s12864-018-5112-0
Towards Predicting Graft Vs Host Disease from Predicted Tissue Specific Minor Histocompatibility Antigens Blood 2018 https://doi.org/10.1182/blood-2018-99-119783
Determining the quantitative principles of T cell response to antigenic disparity in stem cell transplantation Frontiers in immunology 2018 https://doi.org/10.3389/fimmu.2018.02284
ONC201 kills breast cancer cells in vitro by targeting mitochondria Oncotarget 2018 https://doi.org/10.18632/oncotarget.24862
Discovery of Kaposi's sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA Proceedings of the National Academy of Sciences 2018 https://doi.org/10.1073/pnas.1816183115
MEEPTOOLS: a maximum expected error based FASTQ read filtering and trimming toolkit International Journal of Computational Biology and Drug Design 2017 https://doi.org/10.1504/IJCBDD.2017.085409
Dynamical system modeling to simulate donor T cell response to whole exome sequencing-derived recipient peptides: Understanding randomness in alloreactivity incidence following stem cell transplantation PLoS One 2017 https://doi.org/10.1371/journal.pone.0187771
Cytomegalovirus Antigenic Mimicry of Human Alloreactive Peptides: Exploring Cross-Reactivity As a Potential Trigger for Graft Versus Host Disease Biology of Blood and Marrow Transplantation 2017 https://doi.org/10.1016/j.bbmt.2016.12.649
Whole Exome Sequencing to Determine the Likelihood of Graft Versus Host Disease in Stem Cell Transplant Donor-Recipient Pairs Biology of Blood and Marrow Transplantation 2017 https://doi.org/10.1016/j.bbmt.2016.12.650
Whole Exome Sequencing and in silico Determination of the Magnitude of Alloreactive Antigen Presentation on HLA DRB1 in Allogeneic Stem Cell Transplant Recipients Biology of Blood and Marrow Transplantation 2017 https://doi.org/10.1016/j.bbmt.2016.12.339
Sequence homology between HLA-bound cytomegalovirus and human peptides: A potential trigger for alloreactivity PloS one 2017 https://doi.org/10.1371/journal.pone.0178763
Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides Demonstrates Different Alloreactivity Potential in HLA-Matched and-Mismatched Donor–Recipient Pairs Biology of Blood and Marrow Transplantation 2016 https://doi.org/10.1016/j.bbmt.2015.11.1103
MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing BMC bioinformatics 2016 https://doi.org/10.1186/s12859-016-1358-1
Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria Microbiology 2016 https://doi.org/10.1099/mic.0.000238
Identification of a gene in Mycoplasma hominis associated with preterm birth and microbial burden in intraamniotic infection American journal of obstetrics and gynecology 2015 https://doi.org/10.1016/j.ajog.2015.01.032
3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information‚Äêrich hydropathic interaction environments described by maps Proteins: Structure, Function, and Bioinformatics 2015 https://doi.org/10.1002/prot.24813
Exome Sequencing Derived Alloreactivity Potential May Predict Gvhd in Allogeneic Stem Cell Transplantation Blood 2015 https://doi.org/10.1182/blood.V126.23.3078.3078
Peptides Derived from the CMV Proteome Mimic Unique Stem Cell Transplant Recipient Specific Peptides: Possible Role in Eliciting a Pro-Gvh T Cell Response Blood 2015 https://doi.org/10.1182/blood.V126.23.4285.4285
Understanding Water and Its Many Roles in Biological Structure: Ways to Exploit a Resource for Drug Discovery Computer-Aided Drug Discovery 2015 https://doi.org/10.1007/7653_2015_58
Whole exome sequencing to estimate alloreactivity potential between donors and recipients in stem cell transplantation British journal of haematology 2014 https://doi.org/10.1111/bjh.12898
BOTUX: Bayesian-like operational taxonomic unit examiner International journal of computational biology and drug design 2014 https://doi.org/10.1504/IJCBDD.2014.061652
Stem cell transplantation as a dynamical system: are clinical outcomes deterministic? Frontiers in immunology 2014 https://doi.org/10.3389/fimmu.2014.00613
Differences in vaginal microbiome in African American women versus women of European ancestry Microbiology 2014 https://doi.org/10.1099/mic.0.081034-0
In silico derivation of HLA-specific alloreactivity potential from whole exome sequencing of stem-cell transplant donors and recipients: understanding the quantitative immunobiology of allogeneic transplantation Frontiers in immunology 2014 https://doi.org/10.3389/fimmu.2014.00529
Applying an empirical hydropathic forcefield in refinement may improve low-resolution protein X-ray crystal structures PLoS One 2011 https://doi.org/10.1371/journal.pone.0015920
Phase transformations during sintering of titania nanoparticles ACS nano 2008 https://doi.org/10.1021/nn800092m
Sintering of titanium dioxide nanoparticles: a comparison between molecular dynamics and phenomenological modeling Journal of Nanoparticle Research 2008 https://doi.org/10.1007/s11051-007-9342-3
Molecular dynamics study of water adsorption on TiO2 nanoparticles The Journal of Physical Chemistry C 2007 https://doi.org/10.1021/jp0666380
Molecular dynamics simulation of titanium dioxide nanoparticle sintering The Journal of Physical Chemistry B 2005 https://doi.org/10.1021/jp054667p

Pinned Loading

  1. CCBR/Dockers CCBR/Dockers Public

    A collection of Dockerfiles to facilitate reproducibility across computing environments.

    Dockerfile 11 3

  2. CCBR/CARLISLE CCBR/CARLISLE Public

    Cut And Run Analysis Pipeline

    Python 4 4

  3. CCBR/ASCENT CCBR/ASCENT Public

    rMATs and IsoformSwitchAnalyeR workflow for multi-group multi-contrasts scenarios

    Python 2

  4. CCBR/ASPEN CCBR/ASPEN Public

    CCBR pipeline for preliminary QC and peak calling from ATACseq datasets 🌲

    Shell 2

  5. CCBR/CHARLIE CCBR/CHARLIE Public

    Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs

    Python 2 1